RIBD_MAIZE
ID RIBD_MAIZE Reviewed; 392 AA.
AC B6TRH4; B4FA35;
DT 26-JUN-2013, integrated into UniProtKB/Swiss-Prot.
DT 16-DEC-2008, sequence version 1.
DT 03-AUG-2022, entry version 71.
DE RecName: Full=Riboflavin biosynthesis protein PYRD, chloroplastic;
DE Includes:
DE RecName: Full=Diaminohydroxyphosphoribosylaminopyrimidine deaminase;
DE Short=DRAP deaminase;
DE EC=3.5.4.26;
DE AltName: Full=Riboflavin-specific deaminase;
DE Includes:
DE RecName: Full=Inactive 5-amino-6-(5-phosphoribosylamino)uracil reductase;
DE AltName: Full=HTP reductase;
DE Flags: Precursor;
GN Name=PYRD; ORFNames=GRMZM2G320099 {ECO:0000305};
OS Zea mays (Maize).
OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
OC Spermatophyta; Magnoliopsida; Liliopsida; Poales; Poaceae; PACMAD clade;
OC Panicoideae; Andropogonodae; Andropogoneae; Tripsacinae; Zea.
OX NCBI_TaxID=4577;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RX PubMed=18937034; DOI=10.1007/s11103-008-9415-4;
RA Alexandrov N.N., Brover V.V., Freidin S., Troukhan M.E., Tatarinova T.V.,
RA Zhang H., Swaller T.J., Lu Y.-P., Bouck J., Flavell R.B., Feldmann K.A.;
RT "Insights into corn genes derived from large-scale cDNA sequencing.";
RL Plant Mol. Biol. 69:179-194(2009).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC STRAIN=cv. B73;
RX PubMed=19936069; DOI=10.1371/journal.pgen.1000740;
RA Soderlund C., Descour A., Kudrna D., Bomhoff M., Boyd L., Currie J.,
RA Angelova A., Collura K., Wissotski M., Ashley E., Morrow D., Fernandes J.,
RA Walbot V., Yu Y.;
RT "Sequencing, mapping, and analysis of 27,455 maize full-length cDNAs.";
RL PLoS Genet. 5:E1000740-E1000740(2009).
RN [3]
RP SUBCELLULAR LOCATION.
RX PubMed=23150645; DOI=10.1104/pp.112.208488;
RA Hasnain G., Frelin O., Roje S., Ellens K.W., Ali K., Guan J.C.,
RA Garrett T.J., de Crecy-Lagard V., Gregory J.F. III, McCarty D.R.,
RA Hanson A.D.;
RT "Identification and characterization of the missing pyrimidine reductase in
RT the plant riboflavin biosynthesis pathway.";
RL Plant Physiol. 161:48-56(2013).
CC -!- FUNCTION: Monofunctional pyrimidine deaminase involved in the
CC riboflavin biosynthesis pathway. Has also a reductase domain that lacks
CC catalytically essential substrate-binding residues (By similarity).
CC {ECO:0000250}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=2,5-diamino-6-hydroxy-4-(5-phosphoribosylamino)-pyrimidine +
CC H(+) + H2O = 5-amino-6-(5-phospho-D-ribosylamino)uracil + NH4(+);
CC Xref=Rhea:RHEA:21868, ChEBI:CHEBI:15377, ChEBI:CHEBI:15378,
CC ChEBI:CHEBI:28938, ChEBI:CHEBI:58453, ChEBI:CHEBI:58614; EC=3.5.4.26;
CC -!- COFACTOR:
CC Name=Zn(2+); Xref=ChEBI:CHEBI:29105; Evidence={ECO:0000250};
CC Note=Binds 1 zinc ion. {ECO:0000250};
CC -!- PATHWAY: Cofactor biosynthesis; riboflavin biosynthesis; 5-amino-6-(D-
CC ribitylamino)uracil from GTP: step 2/4.
CC -!- SUBCELLULAR LOCATION: Plastid, chloroplast
CC {ECO:0000269|PubMed:23150645}.
CC -!- MISCELLANEOUS: Unlike bacteria that have a bifunctional, two-domain
CC RibD enzyme, plants have a monofunctional reductase and a
CC monofunctional deaminase, each having an enzymatically inactive domain.
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DR EMBL; EU967589; ACG39707.1; -; mRNA.
DR EMBL; BT033973; ACF78978.1; -; mRNA.
DR RefSeq; NP_001130669.1; NM_001137197.1.
DR AlphaFoldDB; B6TRH4; -.
DR SMR; B6TRH4; -.
DR STRING; 4577.GRMZM2G320099_P01; -.
DR PaxDb; B6TRH4; -.
DR GeneID; 100191772; -.
DR KEGG; zma:100191772; -.
DR eggNOG; KOG1018; Eukaryota.
DR HOGENOM; CLU_036590_2_0_1; -.
DR OrthoDB; 619775at2759; -.
DR UniPathway; UPA00275; UER00401.
DR Proteomes; UP000007305; Unplaced.
DR ExpressionAtlas; B6TRH4; baseline and differential.
DR GO; GO:0009507; C:chloroplast; IEA:UniProtKB-SubCell.
DR GO; GO:0008835; F:diaminohydroxyphosphoribosylaminopyrimidine deaminase activity; IBA:GO_Central.
DR GO; GO:0008270; F:zinc ion binding; IEA:InterPro.
DR GO; GO:0009231; P:riboflavin biosynthetic process; IEA:UniProtKB-UniPathway.
DR Gene3D; 3.40.430.10; -; 1.
DR InterPro; IPR016192; APOBEC/CMP_deaminase_Zn-bd.
DR InterPro; IPR002125; CMP_dCMP_dom.
DR InterPro; IPR016193; Cytidine_deaminase-like.
DR InterPro; IPR024072; DHFR-like_dom_sf.
DR InterPro; IPR004794; Eubact_RibD.
DR Pfam; PF00383; dCMP_cyt_deam_1; 1.
DR PIRSF; PIRSF006769; RibD; 1.
DR SUPFAM; SSF53597; SSF53597; 1.
DR SUPFAM; SSF53927; SSF53927; 1.
DR TIGRFAMs; TIGR00326; eubact_ribD; 1.
DR PROSITE; PS00903; CYT_DCMP_DEAMINASES_1; 1.
DR PROSITE; PS51747; CYT_DCMP_DEAMINASES_2; 1.
PE 2: Evidence at transcript level;
KW Chloroplast; Hydrolase; Metal-binding; Plastid; Reference proteome;
KW Transit peptide; Zinc.
FT TRANSIT 1..26
FT /note="Chloroplast"
FT /evidence="ECO:0000255"
FT CHAIN 27..392
FT /note="Riboflavin biosynthesis protein PYRD, chloroplastic"
FT /id="PRO_0000422705"
FT DOMAIN 46..168
FT /note="CMP/dCMP-type deaminase"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01083"
FT ACT_SITE 97
FT /note="Proton donor"
FT /evidence="ECO:0000250"
FT BINDING 95
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000250"
FT BINDING 120
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000250"
FT BINDING 129
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000250"
FT CONFLICT 30
FT /note="A -> V (in Ref. 2; ACF78978)"
FT /evidence="ECO:0000305"
FT CONFLICT 35
FT /note="S -> G (in Ref. 2; ACF78978)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 392 AA; 41834 MW; DD0BA3B63267DDE4 CRC64;
MASSLVSRPH LTQRPVRAAT LASATRPRLA AGALSGRCQA QAAGDLDDAH YMRRCVELAR
KAAGHTSPNP MVGCVIVRDG RVVGEGFHPK AGQPHAEVFA LRDAGNLAEN ATAYVSLEPC
NHYGRTPPCT EALINAKVKE VVVGMTDPNP IVASKGIEKL QGAGISVRVG VEEALCRKLN
EAYIHRMLTG KAFATLRATL SMNGIITNQI GKGADQSGGY YSQLMKEYDG VIISSDLAKM
SALPLSREAG TNQPLCIIIA QGESSRLHIP SLSQEHASRA IVLADSPVTV EPAGVEVAVF
RQIDLESILQ LLAQRGLCSV LVDFREAGES FASLLNDFQE DKLVQKVVVE VLPFWLASDG
LSNLAFGGSQ SFPLKNLELR DVNGSVLLEG YV
